Announcing the worldwide Protein Data Bank

The Protein Data Bank

Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196

The protein data bank: A computer-based archival file for macromolecular structures

Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977) · Journal of Molecular Biology · doi:10.1016/s0022-2836(77)80200-3 · Cited by 8,574

[30] Macromolecular crystallographic information file

Bourne, P. E., Berman, H. M., McMahon, B., Watenpaugh, K. D., Westbrook, J., & Fitzgerald, P. M. D. (1997) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(97)77032-0 · Cited by 170

PubChem: A Large‐Scale Public Chemical Database for Drug Discovery

Kim, S., & Bolton, E. (2023) · Methods and principles in medicinal chemistry · doi:10.1002/9783527830497.ch2 · Cited by 52

Structure, conformational dynamics, quantum mechanical studies and potential biological activity analysis of multiple sclerosis medicine ozanimod

Al‐Zaqri, N., Pooventhiran, T., Rao, D. J., Alsalme, A., Warad, I., & Thomas, R. (2020) · Journal of Molecular Structure · doi:10.1016/j.molstruc.2020.129685 · Cited by 50

A universal programmable Gaussian boson sampler for drug discovery

Yu, S., Zhong, Z., Fang, Y., Patel, R. B., Li, Q., Liu, W., Li, Z., Xu, L., Sagona-Stophel, S., Mer, E., et al. (2023) · Nature Computational Science · doi:10.1038/s43588-023-00526-y · Cited by 60

Comparative evaluation of methods for the prediction of protein–ligand binding sites

Utgés, J. S., & Barton, G. J. (2024) · Journal of Cheminformatics · doi:10.1186/s13321-024-00923-z · Cited by 51

A synthesis, in silico, in vitro and in vivo study of thieno[2,3-b]pyridine anticancer analogues

Arabshahi, H. J., van Rensburg, M., Pilkington, L. I., Jeon, C. Y., Song, M., Gridel, L.-M., Leung, E. Y., Barker, D. L. A., Vuica‐Ross, M., Volcho, K. P., et al. (2015) · MedChemComm · doi:10.1039/c5md00245a · Cited by 50

Norine, the knowledgebase dedicated to non-ribosomal peptides, is now open to crowdsourcing

Flissi, A., Dufresne, Y., Michálik, J., Tonon, L., Janot, S., Noé, L., Jacques, P., Leclère, V., & Pupin, M. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1143 · Cited by 50

Linking Genotype and Phenotype of Saccharomyces cerevisiae Strains Reveals Metabolic Engineering Targets and Leads to Triterpene Hyper-Producers

Madsen, K. M., Udatha, D. B. R. K. G., Semba, S., Otero, J. M., Kötter, P., Nielsen, J., Ebizuka, Y., Kushiro, T., & Panagiotou, G. (2011) · PLoS ONE · doi:10.1371/journal.pone.0014763 · Cited by 50

Automating crystallographic structure solution and refinement of protein–ligand complexes

Echols, N., Moriarty, N. W., Klei, H. E., Afonine, P. V., Bunkòczi, G., Headd, J. J., McCoy, A. J., Oeffner, R. D., Read, R. J., Terwilliger, T. C., et al. (2013) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s139900471302748x · Cited by 49

Pharmacophore-based discovery of FXR agonists. Part I: Model development and experimental validation

Schuster, D., Markt, P., Grienke, U., Mihaly‐Bison, J., Binder, M., Noha, S. M., Rollinger, J. M., Stuppner, H., Bochkov, V. N., & Wolber, G. (2011) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2011.09.056 · Cited by 51

Identification of Coevolving Residues and Coevolution Potentials Emphasizing Structure, Bond Formation and Catalytic Coordination in Protein Evolution

Little, D. Y.-J., & Chen, L. (2009) · PLoS ONE · doi:10.1371/journal.pone.0004762 · Cited by 50

Putative drug and vaccine target protein identification using comparative genomic analysis of KEGG annotated metabolic pathways of Mycoplasma hyopneumoniae

Damte, D., Suh, J., Lee, S., Yohannes, S. B., Hossain, M. A., & Park, S. (2013) · Genomics · doi:10.1016/j.ygeno.2013.04.011 · Cited by 50

Catechol alkenyls from Semecarpus anacardium: Acetylcholinesterase inhibition and binding mode predictions

Adhami, H., Linder, T., Kählig, H., Schuster, D., Zehl, M., & Krenn, L. (2011) · Journal of Ethnopharmacology · doi:10.1016/j.jep.2011.10.032 · Cited by 50

The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites

Cereto‐Massagué, A., Ojeda, M. J., Joosten, R. P., Valls, C., Mulero, M., Salvadó, M. J., Arola‐Arnal, A., Arola, L., Garcı́a-Vallvé, S., & Pujadas, G. (2013) · Journal of Cheminformatics · doi:10.1186/1758-2946-5-36 · Cited by 50

Synthesis of aryl pyrazole via Suzuki coupling reaction, in vitro mushroom tyrosinase enzyme inhibition assay and in silico comparative molecular docking analysis with Kojic acid

Channar, P. A., Saeed, A., Larik, F. A., Batool, B., Kalsoom, S., Hasan, M. M., Erben, M. F., El-Seedi, H. R., Ali, M., & Ashraf, Z. (2018) · Bioorganic Chemistry · doi:10.1016/j.bioorg.2018.04.026 · Cited by 50

Pentagamavunon-1 (PGV-1) inhibits ROS metabolic enzymes and suppresses tumor cell growth by inducing M phase (prometaphase) arrest and cell senescence

Lestari, B., Nakamae, I., Yoneda‐Kato, N., Morimoto, T., Kanaya, S., Yokoyama, T., Shionyu, M., Shirai, T., Meiyanto, E., & Kato, J. (2019) · Scientific Reports · doi:10.1038/s41598-019-51244-3 · Cited by 58

Cannabinoid Receptor Subtype 2 (CB2R) in a Multitarget Approach: Perspective of an Innovative Strategy in Cancer and Neurodegeneration

Mangiatordi, G. F., Intranuovo, F., Delre, P., Abatematteo, F. S., Abate, C., Niso, M., Creanza, T. M., Ancona, N., Stefanachi, A., & Contino, M. (2020) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.0c01357 · Cited by 49

Protein quaternary structures in solution are a mixture of multiple forms

Marciano, S., Dey, D., Listov, D., Fleishman, S. J., Sonn-Segev, A., Mertens, H., Busch, F., Kim, Y., Harvey, S. R., Wysocki, V. H., et al. (2022) · Chemical Science · doi:10.1039/d2sc02794a · Cited by 41

Cyanobacteria as cell factories for the photosynthetic production of sucrose

Santos‐Merino, M., Yun, L., & Ducat, D. C. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1126032 · Cited by 51

Exploring the Molecular Interactions of 7,8-Dihydroxyflavone and Its Derivatives with TrkB and VEGFR2 Proteins

Chitranshi, N., Gupta, V., Kumar, S., & Graham, S. L. (2015) · International Journal of Molecular Sciences · doi:10.3390/ijms160921087 · Cited by 49

Prediction of dinucleotide-specific RNA-binding sites in proteins

Fernández, M., Kumagai, Y., Standley, D. M., Sarai, A., Mizuguchi, K., & Ahmad, S. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-s13-s5 · Cited by 49

Ligand preference and orientation in b‐ and c‐ type heme‐binding proteins

Fufezan, C., Zhang, J., & Gunner, M. R. (2008) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22097 · Cited by 49

Fibronectin Unfolding Revisited: Modeling Cell Traction-Mediated Unfolding of the Tenth Type-III Repeat

Gee, E. P. S., Ingber, D. E., & Stultz, C. M. (2008) · PLoS ONE · doi:10.1371/journal.pone.0002373 · Cited by 51

Recovering physical potentials from a model protein databank

Mullinax, J. W., & Noid, W. G. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1006428107 · Cited by 50

Nuclear Magnetic Resonance Structure and Binding Studies of PqqD, a Chaperone Required in the Biosynthesis of the Bacterial Dehydrogenase Cofactor Pyrroloquinoline Quinone

Evans, R. L., Latham, J. A., Xia, Y., Klinman, J. P., & Wilmot, C. M. (2017) · Biochemistry · doi:10.1021/acs.biochem.7b00247 · Cited by 49

Enzyme Architecture: Modeling the Operation of a Hydrophobic Clamp in Catalysis by Triosephosphate Isomerase

Kulkarni, Y., Liao, Q., Petrović, D., Krüger, D. M., Strodel, B., Amyes, T. L., Richard, J. P., & Kamerlin, S. C. L. (2017) · Journal of the American Chemical Society · doi:10.1021/jacs.7b05576 · Cited by 49

Structural Dynamics of DPP-4 and Its Influence on the Projection of Bioactive Ligands

Pantaleão, S. Q., Philot, E. A., Resende-Lara, P. T., Lima, A. N., Pérahia, D., Miteva, M. A., Scott, A. L., & Honorio, K. M. (2018) · Molecules · doi:10.3390/molecules23020490 · Cited by 49

ETDB-Caltech: A blockchain-based distributed public database for electron tomography

Ortega, D. R., Oikonomou, C. M., Ding, H. J., Rees-Lee, P., Alexandria, & Jensen, G. J. (2019) · PLoS ONE · doi:10.1371/journal.pone.0215531 · Cited by 49

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures

Berman, H. M., Adams, P. D., Bonvin, A. M. J. J., Burley, S. K., Carragher, B. O., Chiu, W., DiMaio, F., Ferrin, T. E., Gabanyi, M. J., Goddard, T. D., et al. (2019) · Structure · doi:10.1016/j.str.2019.11.002 · Cited by 51

The Need for Integrated Approaches in Metabolic EngineeringPreprint

Lechner, A., Brunk, E., & Keasling, J. D. (2016) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a023903 · Cited by 49

Quadratic Binary Programming Models in Computational Biology

Forrester, R. J., & Greenberg, H. J. (2008) · Algorithmic operations research · Cited by 48

In silico exploration of lignin peroxidase for unraveling the degradation mechanism employing lignin model compounds

Singh, A. K., Katari, S. K., Umamaheswari, A., & Raj, A. (2021) · RSC Advances · doi:10.1039/d0ra10840e · Cited by 48

The impact of human leukocyte antigen (HLA) micropolymorphism on ligand specificity within the HLA-B*41 allotypic family

Bade-Doding, C., Theodossis, A., Gras, S., Kjer‐Nielsen, L., Eiz‐Vesper, B., Seltsam, A. W., Huyton, T., Rossjohn, J., McCluskey, J., & Blasczyk, R. (2010) · Haematologica · doi:10.3324/haematol.2010.030924 · Cited by 48

Identifying and Visualizing Macromolecular Flexibility in Structural Biology

Palamini, M., Canciani, A., & Forneris, F. (2016) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2016.00047 · Cited by 51

Antitubulin sulfonamides: The successful combination of an established drug class and a multifaceted target

Vicente‐Blázquez, A., González, M., Álvarez, R., Mazo, S. D., Medarde, M., & Peláez, R. (2018) · Medicinal Research Reviews · doi:10.1002/med.21541 · Cited by 49

Exploring designability of electrostatic complementarity at an antigen-antibody interface directed by mutagenesis, biophysical analysis, and molecular dynamics simulations

Yoshida, K., Kuroda, D., Kiyoshi, M., Nakakido, M., Nagatoishi, S., Soga, S., Shirai, H., & Tsumoto, K. (2019) · Scientific Reports · doi:10.1038/s41598-019-40461-5 · Cited by 49

Promising New Inhibitors of Tyrosyl-DNA Phosphodiesterase I (Tdp 1) Combining 4-Arylcoumarin and Monoterpenoid Moieties as Components of Complex Antitumor Therapy

Khomenko, T. M., Zakharenko, A. L., Chepanova, A. A., Ilina, E. S., Zakharova, O. D., Kaledin, V. I., Nikolin, V. P., Popova, N. A., Викторовна, К. Д., Reynisson, J., et al. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms21010126 · Cited by 48

Single Residue Variation in Skeletal Muscle Myosin Enables Direct and Selective Drug Targeting for Spasticity and Muscle Stiffness

Gyimesi, M., Horváth, Á. I., Túrós, D., Suthar, S. K., Pénzes, M., Kurdi, C., Canon, L., Kikuti, C. M., Ruppel, K. M., Trivedi, D. V., et al. (2020) · Cell · doi:10.1016/j.cell.2020.08.050 · Cited by 48

Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry

Vivoli, M., Novak, H. R., Littlechild, J. A., & Harmer, N. J. (2014) · Journal of Visualized Experiments · doi:10.3791/51809-v · Cited by 48

The chemistry of protein catalysis.

Holliday, G., Almonacid, D., Mitchell, J. B. O., & Thornton, J. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.07.034 · Cited by 42

X-ray crystallographic study of DNA duplex cross-linking: simultaneous binding to two d(CGTACG)2 molecules by a bis(9-aminoacridine-4-carboxamide) derivative

Hopcroft, N. H., Brogden, A. L., Searcey, M., & Cardin, C. J. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl930 · Cited by 48

Sitagliptin: a potential drug for the treatment of COVID-19?

Bardaweel, S. K., Hajjo, R., & Sabbah, D. A. (2020) · Acta Pharmaceutica · doi:10.2478/acph-2021-0013 · Cited by 47

Novel imidazopyrimidines-based molecules induce tetramerization of tumor pyruvate kinase M2 and exhibit potent antiproliferative profile

Patel, S., Globisch, C., Pulugu, P., Kumar, P., Jain, A. K., & Shard, A. (2021) · European Journal of Pharmaceutical Sciences · doi:10.1016/j.ejps.2021.106112 · Cited by 48

Assessing PDB macromolecular crystal structure confidence at the individual amino acid residue level

Shao, C., Bittrich, S., Wang, S., & Burley, S. K. (2022) · Structure · doi:10.1016/j.str.2022.08.004 · Cited by 45

Aspartame carcinogenic potential revealed through network toxicology and molecular docking insights

Chen, D., & Hou, X. (2024) · Scientific Reports · doi:10.1038/s41598-024-62461-w · Cited by 47

A knowledge‐based potential function predicts the specificity and relative binding energy of RNA‐binding proteins

Zheng, S., Robertson, T. A., & Varani, G. (2007) · FEBS Journal · doi:10.1111/j.1742-4658.2007.06155.x · Cited by 47

Soluble polysialylated NCAM: a novel player of the innate immune system in the lung

Ulm, C., Saffarzadeh, M., Mahavadi, P., Müller, S., Prem, G., Saboor, F., Simon, P., Middendorff, R., Geyer, H., Henneke, I., et al. (2013) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-013-1342-0 · Cited by 53

In Silico Identification of Mimicking Molecules as Defense Inducers Triggering Jasmonic Acid Mediated Immunity against Alternaria Blight Disease in Brassica Species

Pathak, R. K., Baunthiyal, M., Shukla, R., Pandey, D., Taj, G., & Kumar, A. (2017) · Frontiers in Plant Science · doi:10.3389/fpls.2017.00609 · Cited by 46

Palladium(II) complexes with salicylaldehyde ligands: Synthesis, characterization, structure, in vitro and in silico study of the interaction with calf-thymus DNA and albumins

Zianna, A., Geromichalos, G. D., Hatzidimitriou, A. G., Coutouli‐Argyropoulou, E., Lalia‐Kantouri, M., & Psomas, G. (2019) · Journal of Inorganic Biochemistry · doi:10.1016/j.jinorgbio.2019.02.013 · Cited by 47

Computational search for potential COVID-19 drugs from FDA-approved drugs and small molecules of natural origin identifies several anti-virals and plant products

Sharma, A., Tiwari, V. R., & Sowdhamini, R. (2020) · Journal of Biosciences · doi:10.1007/s12038-020-00069-8 · Cited by 47

Structural basis for allosteric regulation of pyruvate kinase M2 by phosphorylation and acetylation

Nandi, S., Razzaghi, M., Srivastava, D., & Dey, M. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.ra120.015800 · Cited by 52

EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure RepresentationPreprint

Lee, J. H., Yadollahpour, P., Watkins, A. M., Frey, N. C., Leaver‐Fay, A., Ra, S., Cho, K., Gligorijević, V., Regev, A., & Bonneau, R. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.07.511322 · Cited by 57

On-the-fly QM/MM docking with attracting cavities.

Chaskar, P., Zoete, V., & Röhrig, U. F. (2017) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6b00406 · Cited by 46

Quantum Chemistry Simulation of Biological Molecules

Albuquerque, E. L., Fulco, U. L., Caetano, E. W. S., & Freire, V. N. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108774956 · Cited by 46

Synthesis, structural features, excited state properties, flouresence spectra, and quantum chemical modeling of (E)-2-hydroxy-5-(((4-sulfamoylphenyl)imino) methyl)benzoic acid

Ali, O. A. A., Elangovan, N., Mahmoud, S. F., El‐Bahy, S. M., El-Bahy, Z. M., & Thomas, R. (2022) · Journal of Molecular Liquids · doi:10.1016/j.molliq.2022.119557 · Cited by 47

Solution mapping of T cell receptor docking footprints on peptide-MHC

Varani, L., Bankovich, A. J., Liu, C. W., Colf, L. A., Jones, L. L., Kranz, D. M., Puglisi, J. D., & García, K. C. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0703702104 · Cited by 46

The structure of a prophenoloxidase (PPO) from Anopheles gambiae provides new insights into the mechanism of PPO activation

Hu, Y., Wang, Y., Deng, J., & Jiang, H. (2016) · BMC Biology · doi:10.1186/s12915-015-0225-2 · Cited by 46

Structural and functional features of the NAD(P) dependent Gfo/Idh/MocA protein family oxidoreductases

Taberman, H., Parkkinen, T., & Rouvinen, J. (2016) · Protein Science · doi:10.1002/pro.2877 · Cited by 46

Integrated regulation of the phosphatidylinositol cycle and phosphoinositide‐driven lipid transport at ER‐PM contact sites

Pemberton, J. G., Kim, Y. J., & Balla, T. (2019) · Traffic · doi:10.1111/tra.12709 · Cited by 44

The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies

Waman, V., Sen, N., Váradi, M., Daina, A., Wodak, S. J., Zoete, V., Velankar, S. S., & Orengo, C. A. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa362 · Cited by 45

Structural Genomics and Drug Discovery for Infectious Diseases

Anderson, W. F. (2009) · Infectious Disorders - Drug Targets · doi:10.2174/187152609789105713 · Cited by 45

Using RosettaLigand for Small Molecule Docking into Comparative Models

Kaufmann, K. W., & Meiler, J. (2012) · PLoS ONE · doi:10.1371/journal.pone.0050769 · Cited by 44

Predicting small ligand binding sites in proteins using backbone structure

Bordner, A. J. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn543 · Cited by 46

A new residue‐nucleotide propensity potential with structural information considered for discriminating protein‐RNA docking decoys

Li, C. H., Cao, L. B., Su, J. G., Yang, Y. X., & Wang, C. X. (2011) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.23117 · Cited by 46

Discovery of a new class of reversible TEA domain transcription factor inhibitors with a novel binding mode

Hu, L., Sun, Y., Liu, S., Erb, H., Singh, A., Mao, J., Luo, X., & Wu, X. (2022) · eLife · doi:10.7554/elife.80210 · Cited by 49

The Bright Side of Psychedelics: Latest Advances and Challenges in Neuropharmacology

Mastinu, A., Anyanwu, M., Carone, M., Abate, G., Bonini, S. A., Peron, G., Tirelli, E., Pucci, M., Ribaudo, G., Oselladore, E., et al. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24021329 · Cited by 52

Recent Developments in Ultralarge and Structure-Based Virtual Screening Approaches

Gorgulla, C. (2023) · Annual Review of Biomedical Data Science · doi:10.1146/annurev-biodatasci-020222-025013 · Cited by 58

A model of dirigent proteins derived from structural and functional similarities with allene oxide cyclase and lipocalins

Pickel, B., Pfannstiel, J., Steudle, A., Lehmann, A., Gerken, U., Pleiss, J., & Schaller, A. (2012) · FEBS Journal · doi:10.1111/j.1742-4658.2012.08580.x · Cited by 45

Data management challenges in three-dimensional EM

Patwardhan, A., Carazo, J. M., Carragher, B. O., Henderson, R. A., Heymann, J. B., Hill, E., Jensen, G. J., Lagerstedt, I. C., Lawson, C. L., Ludtke, S. J., et al. (2012) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2426 · Cited by 45

Federated repositories of X-ray diffraction images

Androulakis, S., Schmidberger, J. W., Bate, M. A., DeGori, R., Beitz, A., Keong, C., Cameron, B., McGowan, S., Porter, C. J., Harrison, A., et al. (2008) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444908015540 · Cited by 45

HOMCOS: an updated server to search and model complex 3D structures

Kawabata, T. (2016) · Journal of Structural and Functional Genomics · doi:10.1007/s10969-016-9208-y · Cited by 45

New Hydrazinothiazole Derivatives of Usnic Acid as Potent Tdp1 Inhibitors

Filimonov, A. S., Chepanova, A. A., Luzina, O. A., Zakharenko, A. L., Zakharova, O. D., Ilina, E. S., Dyrkheeva, N. S., Kupryushkin, M. S., Колотаев, А. В., Khachatryan, D. S., et al. (2019) · Molecules · doi:10.3390/molecules24203711 · Cited by 45

The biomedical and bioengineering potential of protein nanocompartments

Demchuk, A. M., & Patel, T. R. (2020) · Biotechnology Advances · doi:10.1016/j.biotechadv.2020.107547 · Cited by 45

Functional characterization of rare NRXN1 variants identified in autism spectrum disorders and schizophrenia

Ishizuka, K., Yoshida, T., Kawabata, T., Imai, A., Mori, H., Kimura, H., Inada, T., Okahisa, Y., Egawa, J., Usami, M., et al. (2020) · Journal of Neurodevelopmental Disorders · doi:10.1186/s11689-020-09325-2 · Cited by 49

Mapping and Validation of scRNA-Seq-Derived Cell-Cell Communication Networks in the Tumor Microenvironment

Bridges, K., & Miller‐Jensen, K. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.885267 · Cited by 48

General mutation databases: analysis and review

George, R. A., Smith, T. D., Callaghan, S., Hardman, L., Pierides, C., Horaitis, O., Wouters, M. A., & Cotton, R. G. H. (2007) · Journal of Medical Genetics · doi:10.1136/jmg.2007.052639 · Cited by 45

Electrochemically Driven Photosynthetic Electron Transport in Cyanobacteria Lacking Photosystem II

Lewis, C. M., Flory, J., Moore, T. A., Moore, A. L., Rittmann, B. E., Vermaas, W. F. J., Torres, C. I., & Fromme, P. (2022) · Journal of the American Chemical Society · doi:10.1021/jacs.1c09291 · Cited by 44

CHARMM-GUI PDB Reader and Manipulator: Covalent Ligand Modeling and Simulation

Kong, L., Park, S., & Im, W. (2024) · Journal of Molecular Biology · doi:10.1016/j.jmb.2024.168554 · Cited by 47

Protein Data Bank (PDB): Fifty-three years young and having a transformative impact on science and society

Berman, H. M., & Burley, S. K. (2025) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583525000034 · Cited by 49

X ‐ray structure of a protease‐resistant mutant form of human galectin‐8 with two carbohydrate recognition domains

Yoshida, H., Yamashita, S., Teraoka, M., Itoh, A., Nakakita, S., Nishi, N., & Kamitori, S. (2012) · FEBS Journal · doi:10.1111/j.1742-4658.2012.08753.x · Cited by 46

Solid−Solid Interface Adsorption of Proteins and Enzymes in Nanophase-Separated Amphiphilic Conetworks

Dech, S., Cramer, T., Ladisch, R., Bruns, N., & Tiller, J. C. (2011) · Biomacromolecules · doi:10.1021/bm1015877 · Cited by 44

A-to-I and C-to-U editing within transfer RNAs

Su, A. A. H., & Randau, L. (2011) · Biochemistry (Moscow) · doi:10.1134/s0006297911080098 · Cited by 44

Ligand Entropy in Gas-Phase, Upon Solvation and Protein Complexation. Fast Estimation with Quasi-Newton Hessian

Wlodek, S. T., Skillman, A. G., & Nicholls, A. O. (2010) · Journal of Chemical Theory and Computation · doi:10.1021/ct100095p · Cited by 44

Distributions of enzyme residues yielding mutants with improved substrate specificities from two different directed evolution strategies

Paramesvaran, J., Hibbert, E. G., Russell, A. J., & Dalby, P. A. (2009) · Protein Engineering Design and Selection · doi:10.1093/protein/gzp020 · Cited by 44

Disulfide Scrambling in IgG2 Monoclonal Antibodies: Insights from Molecular Dynamics Simulations

Wang, X., Kumar, S., & Singh, S. K. (2011) · Pharmaceutical Research · doi:10.1007/s11095-011-0503-9 · Cited by 44

PROCOGNATE: a cognate ligand domain mapping for enzymes

Bashton, M., Nobeli, I., & Thornton, J. M. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm611 · Cited by 44

Effect of ATP Binding and Hydrolysis on Dynamics of Canine Parvovirus NS1

Niskanen, E. A., Ihalainen, T. O., Kalliolinna, O., Häkkinen, M., & Vihinen‐Ranta, M. (2010) · Journal of Virology · doi:10.1128/jvi.02221-09 · Cited by 44

In Silico Approach to Find Chymase Inhibitors Among Biogenic Compounds

Dubey, A., Facchiano, A. M., Ramteke, P. W., & Marabotti, A. (2016) · Future Medicinal Chemistry · doi:10.4155/fmc-2016-0030 · Cited by 44

Building Models Using Reactome Pathways as Templates

Croft, D. W. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-450-0_14 · Cited by 44

Adaptive thermostability of light-harvesting complexes in marine picocyanobacteria

Pittera, J., Partensky, F., & Six, C. (2016) · The ISME Journal · doi:10.1038/ismej.2016.102 · Cited by 43

The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling

Viswanath, S., Bonomi, M., Kim, S. J., Klenchin, V. A., Taylor, K. C., Yabut, K. C. B., Umbreit, N. T., Epps, H. A. V., Meehl, J. B., Jones, M. H., et al. (2017) · Molecular Biology of the Cell · doi:10.1091/mbc.e17-06-0397 · Cited by 44

Insight into small molecule binding to the neonatal Fc receptor by X-ray crystallography and 100 kHz magic-angle-spinning NMR

Friedrich, D., Macpherson, A., Penzel, S., Basse, N., Lecomte, F., Deboves, H., Taylor, R. D., Norman, T., Porter, J. R., Waters, L. C., et al. (2018) · PLoS Biology · doi:10.1371/journal.pbio.2006192 · Cited by 44

Identification, structure analysis, and transcript profiling of purple acid phosphatases under Pi deficiency in tomato (Solanum lycopersicum L.) and its wild relatives

Srivastava, R., Akash, A., Parida, A. P., Chauhan, P. K., & Kumar, R. (2020) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2020.10.080 · Cited by 44

Evaluating the performance of drug-repurposing technologies

Schuler, J., Falls, Z., Mangione, W., Hudson, M. L., Bruggemann, L., & Samudrala, R. (2021) · Drug Discovery Today · doi:10.1016/j.drudis.2021.08.002 · Cited by 43

Allosteric control of Ubp6 and the proteasome via a bidirectional switch

Hung, K. Y. S., Klumpe, S., Eisele, M. R., Elsasser, S., Tian, G., Sun, S., Moroco, J. A., Cheng, T. C., Joshi, T., Seibel, T., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28186-y · Cited by 44

Synthesis and biological assessment of novel 2-thiazolylhydrazones and computational analysis of their recognition by monoamine oxidase B

Distinto, S., Yáñez, M., Alcaro, S., Cardia, M. C., Gaspari, M., Sanna, M. L., Meleddu, R., Ortuso, F., Kirchmair, J., Markt, P., et al. (2011) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2011.12.027 · Cited by 44

Dynameomics: design of a computational lab workflow and scientific data repository for protein simulations

Simms, A. M., Toofanny, R. D., Kehl, C. E., Benson, N. C., & Daggett, V. (2008) · Protein Engineering Design and Selection · doi:10.1093/protein/gzn012 · Cited by 44

Engineering P450 Monooxygenases for Highly Regioselective and Active p -Hydroxylation of m -Alkylphenols

Li, R., Tian, K., Li, X., Gaikaiwari, A. R., & Li, Z. (2022) · ACS Catalysis · doi:10.1021/acscatal.1c06011 · Cited by 44

Highly accurate carbohydrate-binding site prediction with DeepGlycanSite

He, X., Zhao, L.-F., Tian, Y.-P., Li, R., Chu, Q., Gu, Z.-Y., Zheng, M.-Y., Wang, Y., Li, S.-N., Jiang, H.-L., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-49516-2 · Cited by 43

A 3D cellular context for the macromolecular world

Patwardhan, A., Ashton, A., Brandt, R., Butcher, S. J., Carzaniga, R., Chiu, W., Collinson, L., Doux, P., Duke, E., Ellisman, M. H., et al. (2014) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2897 · Cited by 43

Prediction of Detailed Enzyme Functions and Identification of Specificity Determining Residues by Random Forests

Nagao, C., Nagano, N., & Mizuguchi, K. (2014) · PLoS ONE · doi:10.1371/journal.pone.0084623 · Cited by 43

The Worldwide Protein Data Bank

Berman, H. M., Henrick, K., Kleywegt, G. J., Nakamura, H., & Markley, J. L. (2012) · International Tables for Crystallography · doi:10.1107/97809553602060000896 · Cited by 29

The future of the protein data bank

Berman, H. M., Kleywegt, G. J., Nakamura, H., & Markley, J. L. (2012) · Biopolymers · doi:10.1002/bip.22132 · Cited by 80

The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

Berman, H. M., Henrick, K., Nakamura, H., & Markley, J. L. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl971 · Cited by 1,124

Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive

Burley, S. K., Berman, H. M., Kleywegt, G. J., Markley, J. L., Nakamura, H., & Velankar, S. (2017) · Methods in Molecular Biology · doi:10.1007/978-1-4939-7000-1_26 · Cited by 1,141

Abstract 2370 RCSB Protein Data Bank: Updated resources and new developments driving research and education in the biosciences

Zardecki, C., Duarte, J. M., Raymond, D., Rose, Y., Young, J. Y., & Burley, S. K. (2026) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2026.112700 · Cited by 1